The major genetic risk factor for severe COVID-19 does not show any association among South Asian populations

With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50 kb genomic segment introgressed from Neanderthal adding a risk for COVID-19, and this genomic segment is present among 16% and 50% people of European and South Asian descent, respectively. Our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations, respectively, which appears to be responsible for the low case fatality rate among South Asian populations. This result was also consistent with the real-time infection rate and case fatality rate among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the real-time infection rates and case fatality rate in India. We found that the polymorphism present in the 50 kb introgressed genomic segment (rs10490770) did not show any significant correlation with the infection and case fatality rate in India.

Whole Genome Sequencing and Analysis of Mycobacteroides chelonae M77 Isolated from Cow Milk from the Hill State of Meghalaya, India

Background: Mycobacteroides chelonae M77 isolated in a targeted Mycobacterial isolation study from bovine raw milk was whole genome sequenced (CP041150.1), followed by comparative genomics study for better understanding of the organism with special focus on its virulence and antibiotic resistance pattern. This is probably the first whole genome sequence (WGS) of M.cheloane submitted in NCBI database from India. Methods: The WGS has been carried out in Illumina Next Seq 500 platform and then assembled resulting in a genome of 5.12 MB. The assembled genome was annotated in RASTtk and viewed by SEED for its detailed analysis. Pathogen Finder 1.1 and Res Finder 3.1 soft wares were applied for knowing the isolate pathogenecity and antibiotic profiling respectively. Mauve analysis was carried out to know the genomic re-arrangements.Result: Pathogen Finder 1.1 showed that M77 was non-pathogenic and Res Finder 3.1 server reveals it is susceptible to most of the antibiotics. Mauve analysis for alignment of isolate revealed no significant re-arrangement of genomic segment. The whole analysis showed that the genome of M77 is tight genome with not much variation in relation to previous complete genomes reported and is non-pathogenic and sensitive to most of the antibiotics.

Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

Rapid detection of SARS-CoV-2 viral nucleic acids based on surface enhanced infrared absorption spectroscopy

A rapid and sensitive SEIRA-based method for SARS-CoV-2 detection is proposed and analyzed. The proposed method can effectively detect as low as 2.98 copies per μL (∼5 aM) SARS-CoV-2 viral genomic segment within 30 minutes.

The major genetic risk factor for severe COVID-19 is inherited from Neandertals

A recent genetic association study (Ellinghaus et al. 2020) identified a gene cluster on chromosome 3 as a risk locus for respiratory failure in SARS-CoV-2. Recent data comprising 3,199 hospitalized COVID-19 patients and controls reproduce this and find that it is the major genetic risk factor for severe SARS-CoV-2 infection and hospitalization (COVID-19 Host Genetics Initiative). Here, we show that the risk is conferred by a genomic segment of ~50 kb that is inherited from Neandertals and occurs at a frequency of ~30% in south Asia and ~8% in Europe.

The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes

Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two Takifugu are likely the same, but the genes used for the similar phenotype in Takifugu and distantly related fishes are not the same. Meanwhile, Fgfrl1, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since Fgfr1a1, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to Takifugu, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development.